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Is there a reason why you must use restraints with metal coordination?
The main reasons that you use restraints in protein refinement is to
reduce the number of free variables in the refinement, and because the
"resolution" isn't sufficient to resolve two atoms separated by the
typical carbon-carbon distance of 1.5A.
In a metal complex, the distances are roughly 2A or greater, and the metal
position is well-determined since it has a large number of electrons. I
would just restrain the protein part of the structure, and let the metal
refine freely.
Bernie Santarsiero
On Fri, June 7, 2013 9:25 am, Roger Rowlett wrote:
> Well, when I solved a structure for a protein-rhenium adduct I had to
> manually code a restraint file for the rhenium tricarbonyl fragment,
> which is octahedral overall (with proteins ligands and waters), and had
> several different types of bond distances for the various ligands. I
> started with an incorrect description of a similar ligand cif file from
> HIC-UP and hand-edited the cif file to suit. It seems to me it should be
> possible (although somewhat painful) to write a similar restraint file
> (geometry + bond lengths) for ZN.
>
> Cheers,
>
> _______________________________________
> Roger S. Rowlett
> Gordon & Dorothy Kline Professor
> Department of Chemistry
> Colgate University
> 13 Oak Drive
> Hamilton, NY 13346
>
> tel: (315)-228-7245
> ofc: (315)-228-7395
> fax: (315)-228-7935
> email: [log in to unmask]
>
> On 6/7/2013 9:23 AM, Tim Gruene wrote:
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> Hi Jim,
>>
>> the chemical basis would be that the Zn connects to all four S atoms,
>> and if they are indistinguishable, all Zn-S distances should be alike.
>>
>> But the S-atoms are not bonded to each other, hence they want to have as
>> much distance from each other as possible. Since they are four, this
>> makes them a tetrahedron.
>>
>> I am not aware of a more automated/ simpler way of turning the angles
>> at the metal into restraints other than calculating the S-S distances
>> with a pocket calculator, although that does not mean they do not exist.
>>
>> Cheers,
>> Tim
>>
>> On 06/07/2013 11:56 AM, James Naismith wrote:
>>> Andrew Leslie made a similar suggestion for using CB to S
>>> distances.
>>>
>>> Both make me unhappy for the reason that there is not a clear
>>> chemical basis to them (Tim's has more a chemical basis) and how
>>> would I choose the distance. (I can measure it from a known
>>> structure)
>>>
>>>
>>> I have previously experimented with Tim's (works). I am searching
>>> for anyone who knew a simple way to restrain metal ion geometry in
>>> remfac based on angles at metal.
>>>
>>> best Jim
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 7 Jun 2013, at 10:14, Tim Gruene <[log in to unmask]>
>>> wrote:
>>>
>>> Dear James,
>>>
>>> I am not sure I fully picture what your coordination looks like,
>>> but my guess is that if you include distance restraints between the
>>> S-atoms you can distinguish between a tetrahedral geometry and a
>>> square pyramid.
>>>
>>> You could use external restraints in refmac - just make a dummy
>>> run with prosmat to get the syntax right and copy and modify a few
>>> lines tailored to your problem.
>>>
>>> Best, Tim
>>>
>>> On 06/07/2013 10:39 AM, James Naismith wrote:
>>>>>> Thanks for this other suggestions similar (see below.) My
>>>>>> problem is not the distances per se, these restrain fine to
>>>>>> 2.3A
>>>>>>
>>>>>> I am relatively low resolution and my problem is with just
>>>>>> distance restraints I move to a square planar arrangement. I
>>>>>> suspect this is a feature of the geometry restraints
>>>>>> dominating refinement (c'est la vie at low res). I do not
>>>>>> force Zn to be anything (the cif file just has a distance) I
>>>>>> think.
>>>>>>
>>>>>> What I need to do is create another restraint someone how
>>>>>> that imposes a Td geometry.
>>>>>>
>>>>>> What I cannot figure how to do is set this up because it
>>>>>> involves 5 residues (4 cys and 1 Zn).
>>>>>>
>>>>>> best Jim
>>>>>>
>>>>>> Jim Naismith BSRC, North Haugh [log in to unmask]
>>>>>>
>>>>>> Google scholar is free and tracks your outputs, mine are
>>>>>> http://scholar.google.co.uk/citations?hl=en&user=fLmKKQMAAAAJ
>>>>>>
>>>>>>
>>>>>>
>> ResearcherID H-3408-2012; SCOPUS_ID 7005691850
>>>>>> http://www.researchgate.net/profile/James_Naismith/
>>>>>>
>>>>>> The University of St Andrews is a charity registered in
>>>>>> Scotland : No SC013532k
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 6 Jun 2013, at 16:11, Roger Rowlett
>>>>>> <[log in to unmask]> wrote:
>>>>>>
>>>>>>> You can find instructions for restraining Zn-ligand
>>>>>>> distances here:
>>>>>>>
>>>>>>> http://capsicum.colgate.edu/chwiki/tiki-index.php?page=Model+Refinement&highlight=metal%20ion#Restraining_metal_ligand_distances_during_refinement_in_REFMAC
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>> Using this method, only Zn-ligand bond distances are restrained.
>>> REFMAC can usually find on its own certain Zn-atom linkages (I
>>> think it can find ZN-SG bonds with Cys by itself, but the version
>>> I am using usually misses or ZN-OD1 or ZN-OD2 bonds with Asp. This
>>> I pick up in the .cif file generated by REFMAC and include in a
>>> library file to be used for refinement. I have not had any issues
>>> with REFMAC altering ZN geometry. What you describe sounds like
>>> the geometry of the ZN atom has been defined or assumed somewhere
>>> in your approach.
>>>>>>> Cheers,
>>>>>>>
>>>>>>> _______________________________________ Roger S. Rowlett
>>>>>>> Gordon & Dorothy Kline Professor Department of Chemistry
>>>>>>> Colgate University 13 Oak Drive Hamilton, NY 13346
>>>>>>>
>>>>>>> tel: (315)-228-7245 ofc: (315)-228-7395 fax:
>>>>>>> (315)-228-7935 email: [log in to unmask]
>>>>>>>
>>>>>>> On 6/6/2013 10:36 AM, James Naismith wrote:
>>>>>>>> I have a structure that I am trying to finish off, I have
>>>>>>>> Zn ligated by four cys residues. I use the linkR and
>>>>>>>> define distances (the same link for each ZnS bond) My
>>>>>>>> issue is how to stop the structure moving to a square
>>>>>>>> pyramid (consistent with distance restraints) rather
>>>>>>>> than a tetrahedral geometry. Can anyone help?
>>>>>>>>
>>>>>>>> best Jim
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